## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: VST

Gene dynamics (TSS ~ TES)

Those reads were counted only, where both the 3-prime AND the 5-prime adapters were “correct” (according to LoRTIA)

When counting with either adapters, the clustering grouped ORF64 together with two late genes

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.2)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si       se.au
##       <int>  <char>     <num>     <num>     <num>       <num>       <num>
##  1:       1    ORF1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  2:       1    ORF4 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  3:       1    ORF7 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  4:       1    ORF9 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  5:       1   ORF17 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  6:       1   ORF18 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  7:       1   ORF20 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  8:       1   ORF21 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  9:       1   ORF24 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 10:       1   ORF28 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 11:       1   ORF31 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 12:       1   ORF32 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 13:       1   ORF34 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 14:       1   ORF38 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 15:       1   ORF50 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 16:       1   ORF61 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 17:       1 ORF64_1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 18:       1 ORF67_1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 19:       1   ORF74 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 20:       1   ORF75 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 21:       1  NOIR_2 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 22:       2    ORF2 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 23:       2    ORF3 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 24:       2    ORF8 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 25:       2   ORF11 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 26:       2   ORF19 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 27:       2   ORF22 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 28:       2   ORF26 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 29:       2   ORF29 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 30:       2   ORF36 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 31:       2   ORF37 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 32:       2     CTO 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 33:       2   ORF40 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 34:       2   ORF51 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 35:       2 ORF66_1 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 36:       2   ORF73 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 37:       2   ORF76 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 38:       3    ORF5 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 39:       3   ORF30 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 40:       3   ORF53 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 41:       3   ORF63 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 42:       3 ORF65_1 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 43:       3   ORF69 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 44:       4    ORF6 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 45:       4   ORF13 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 46:       4   ORF15 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 47:       4   ORF16 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 48:       4   ORF25 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 49:       4   ORF33 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 50:       4 ORF35.5 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 51:       4   ORF42 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 52:       4   ORF43 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 53:       4   ORF46 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 54:       4   ORF52 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 55:       4   ORF54 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 56:       4   ORF58 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 57:       4   ORF60 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 58:       4   ORF62 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 59:       4   ORF72 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 60:       5   ORF10 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 61:       5   ORF12 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 62:       5   ORF14 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 63:       5   ORF23 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 64:       5   ORF27 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 65:       5   ORF35 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 66:       5   ORF39 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 67:       5   ORF41 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 68:       5   ORF44 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 69:       5   ORF48 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 70:       5   ORF49 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 71:       5   ORF57 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 72:       5   ORF59 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 73:       5  NOIR_1 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 74:       5   ORF68 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 75:       5   ORF70 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 76:       5   ORF71 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
##     cluster    gene        si        au        bp       se.si       se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.005240502 -0.3857226 0.2263551 0.4554380
##  2: 0.005240502 -0.3857226 0.2263551 0.4554380
##  3: 0.005240502 -0.3857226 0.2263551 0.4554380
##  4: 0.005240502 -0.3857226 0.2263551 0.4554380
##  5: 0.005240502 -0.3857226 0.2263551 0.4554380
##  6: 0.005240502 -0.3857226 0.2263551 0.4554380
##  7: 0.005240502 -0.3857226 0.2263551 0.4554380
##  8: 0.005240502 -0.3857226 0.2263551 0.4554380
##  9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.005240502 -0.3857226 0.2263551 0.4554380
## 14: 0.005240502 -0.3857226 0.2263551 0.4554380
## 15: 0.005240502 -0.3857226 0.2263551 0.4554380
## 16: 0.005240502 -0.3857226 0.2263551 0.4554380
## 17: 0.005240502 -0.3857226 0.2263551 0.4554380
## 18: 0.005240502 -0.3857226 0.2263551 0.4554380
## 19: 0.005240502 -0.3857226 0.2263551 0.4554380
## 20: 0.005240502 -0.3857226 0.2263551 0.4554380
## 21: 0.005240502 -0.3857226 0.2263551 0.4554380
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.004740574 -1.0188938 0.3891921 0.7676649
## 25: 0.004740574 -1.0188938 0.3891921 0.7676649
## 26: 0.004740574 -1.0188938 0.3891921 0.7676649
## 27: 0.004740574 -1.0188938 0.3891921 0.7676649
## 28: 0.004740574 -1.0188938 0.3891921 0.7676649
## 29: 0.004740574 -1.0188938 0.3891921 0.7676649
## 30: 0.004740574 -1.0188938 0.3891921 0.7676649
## 31: 0.004740574 -1.0188938 0.3891921 0.7676649
## 32: 0.004740574 -1.0188938 0.3891921 0.7676649
## 33: 0.004740574 -1.0188938 0.3891921 0.7676649
## 34: 0.004740574 -1.0188938 0.3891921 0.7676649
## 35: 0.004740574 -1.0188938 0.3891921 0.7676649
## 36: 0.004740574 -1.0188938 0.3891921 0.7676649
## 37: 0.004740574 -1.0188938 0.3891921 0.7676649
## 38: 0.005096736 -0.1004869 0.4195148 0.9429681
## 39: 0.005096736 -0.1004869 0.4195148 0.9429681
## 40: 0.005096736 -0.1004869 0.4195148 0.9429681
## 41: 0.005096736 -0.1004869 0.4195148 0.9429681
## 42: 0.005096736 -0.1004869 0.4195148 0.9429681
## 43: 0.005096736 -0.1004869 0.4195148 0.9429681
## 44: 0.004909730 -1.3643003 0.7964977 0.0290061
## 45: 0.004909730 -1.3643003 0.7964977 0.0290061
## 46: 0.004909730 -1.3643003 0.7964977 0.0290061
## 47: 0.004909730 -1.3643003 0.7964977 0.0290061
## 48: 0.004909730 -1.3643003 0.7964977 0.0290061
## 49: 0.004909730 -1.3643003 0.7964977 0.0290061
## 50: 0.004909730 -1.3643003 0.7964977 0.0290061
## 51: 0.004909730 -1.3643003 0.7964977 0.0290061
## 52: 0.004909730 -1.3643003 0.7964977 0.0290061
## 53: 0.004909730 -1.3643003 0.7964977 0.0290061
## 54: 0.004909730 -1.3643003 0.7964977 0.0290061
## 55: 0.004909730 -1.3643003 0.7964977 0.0290061
## 56: 0.004909730 -1.3643003 0.7964977 0.0290061
## 57: 0.004909730 -1.3643003 0.7964977 0.0290061
## 58: 0.004909730 -1.3643003 0.7964977 0.0290061
## 59: 0.004909730 -1.3643003 0.7964977 0.0290061
## 60: 0.004107492 -1.6060807 0.6281863 0.3548128
## 61: 0.004107492 -1.6060807 0.6281863 0.3548128
## 62: 0.004107492 -1.6060807 0.6281863 0.3548128
## 63: 0.004107492 -1.6060807 0.6281863 0.3548128
## 64: 0.004107492 -1.6060807 0.6281863 0.3548128
## 65: 0.004107492 -1.6060807 0.6281863 0.3548128
## 66: 0.004107492 -1.6060807 0.6281863 0.3548128
## 67: 0.004107492 -1.6060807 0.6281863 0.3548128
## 68: 0.004107492 -1.6060807 0.6281863 0.3548128
## 69: 0.004107492 -1.6060807 0.6281863 0.3548128
## 70: 0.004107492 -1.6060807 0.6281863 0.3548128
## 71: 0.004107492 -1.6060807 0.6281863 0.3548128
## 72: 0.004107492 -1.6060807 0.6281863 0.3548128
## 73: 0.004107492 -1.6060807 0.6281863 0.3548128
## 74: 0.004107492 -1.6060807 0.6281863 0.3548128
## 75: 0.004107492 -1.6060807 0.6281863 0.3548128
## 76: 0.004107492 -1.6060807 0.6281863 0.3548128
##           se.bp          v         c      pchi

## [1] "ORF32" "ORF74" "ORF75" "ORF28" "ORF24" "ORF76" "ORF37" "ORF25" "ORF14"
## [1] 9
##  [1] "ORF1"    "ORF4"    "ORF7"    "ORF9"    "ORF17"   "ORF18"   "ORF20"  
##  [8] "ORF21"   "ORF24"   "ORF28"   "ORF31"   "ORF32"   "ORF34"   "ORF38"  
## [15] "ORF50"   "ORF61"   "ORF64_1" "ORF67_1" "ORF74"   "ORF75"   "NOIR_2" 
## [22] "ORF2"    "ORF3"    "ORF8"    "ORF11"   "ORF19"   "ORF22"   "ORF26"  
## [29] "ORF29"   "ORF36"   "ORF37"   "CTO"     "ORF40"   "ORF51"   "ORF66_1"
## [36] "ORF73"   "ORF76"   "ORF5"    "ORF30"   "ORF53"   "ORF63"   "ORF65_1"
## [43] "ORF69"
## [1] 43

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si       se.au
##       <int>  <char>     <num>     <num>     <num>       <num>       <num>
##  1:       1    ORF1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  2:       1    ORF4 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  3:       1    ORF7 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  4:       1    ORF9 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  5:       1   ORF17 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  6:       1   ORF18 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  7:       1   ORF20 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  8:       1   ORF21 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
##  9:       1   ORF24 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 10:       1   ORF28 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 11:       1   ORF31 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 12:       1   ORF32 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 13:       1   ORF34 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 14:       1   ORF38 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 15:       1   ORF50 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 16:       1   ORF61 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 17:       1 ORF64_1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 18:       1 ORF67_1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 19:       1   ORF74 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 20:       1   ORF75 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 21:       1  NOIR_2 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 22:       2    ORF2 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 23:       2    ORF3 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 24:       2    ORF8 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 25:       2   ORF11 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 26:       2   ORF19 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 27:       2   ORF22 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 28:       2   ORF26 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 29:       2   ORF29 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 30:       2   ORF36 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 31:       2   ORF37 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 32:       2     CTO 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 33:       2   ORF40 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 34:       2   ORF51 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 35:       2 ORF66_1 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 36:       2   ORF73 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 37:       2   ORF76 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 38:       3    ORF5 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 39:       3   ORF30 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 40:       3   ORF53 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 41:       3   ORF63 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 42:       3 ORF65_1 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 43:       3   ORF69 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 44:       4    ORF6 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 45:       4   ORF13 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 46:       4   ORF15 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 47:       4   ORF16 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 48:       4   ORF33 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 49:       4   ORF42 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 50:       4   ORF52 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 51:       4   ORF54 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 52:       4   ORF60 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 53:       4   ORF72 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 54:       5   ORF10 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 55:       5   ORF12 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 56:       5   ORF14 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 57:       5   ORF23 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 58:       5   ORF27 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 59:       5   ORF35 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 60:       5   ORF39 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 61:       5   ORF41 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 62:       5   ORF44 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 63:       5   ORF48 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 64:       5   ORF49 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 65:       5   ORF57 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 66:       5   ORF59 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 67:       5  NOIR_1 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 68:       5   ORF68 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 69:       5   ORF70 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 70:       5   ORF71 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 71:       6   ORF25 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## 72:       6 ORF35.5 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## 73:       6   ORF43 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## 74:       6   ORF46 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## 75:       6   ORF58 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## 76:       6   ORF62 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
##     cluster    gene        si        au        bp       se.si       se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.005240502 -0.3857226 0.2263551 0.4554380
##  2: 0.005240502 -0.3857226 0.2263551 0.4554380
##  3: 0.005240502 -0.3857226 0.2263551 0.4554380
##  4: 0.005240502 -0.3857226 0.2263551 0.4554380
##  5: 0.005240502 -0.3857226 0.2263551 0.4554380
##  6: 0.005240502 -0.3857226 0.2263551 0.4554380
##  7: 0.005240502 -0.3857226 0.2263551 0.4554380
##  8: 0.005240502 -0.3857226 0.2263551 0.4554380
##  9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.005240502 -0.3857226 0.2263551 0.4554380
## 14: 0.005240502 -0.3857226 0.2263551 0.4554380
## 15: 0.005240502 -0.3857226 0.2263551 0.4554380
## 16: 0.005240502 -0.3857226 0.2263551 0.4554380
## 17: 0.005240502 -0.3857226 0.2263551 0.4554380
## 18: 0.005240502 -0.3857226 0.2263551 0.4554380
## 19: 0.005240502 -0.3857226 0.2263551 0.4554380
## 20: 0.005240502 -0.3857226 0.2263551 0.4554380
## 21: 0.005240502 -0.3857226 0.2263551 0.4554380
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.004740574 -1.0188938 0.3891921 0.7676649
## 25: 0.004740574 -1.0188938 0.3891921 0.7676649
## 26: 0.004740574 -1.0188938 0.3891921 0.7676649
## 27: 0.004740574 -1.0188938 0.3891921 0.7676649
## 28: 0.004740574 -1.0188938 0.3891921 0.7676649
## 29: 0.004740574 -1.0188938 0.3891921 0.7676649
## 30: 0.004740574 -1.0188938 0.3891921 0.7676649
## 31: 0.004740574 -1.0188938 0.3891921 0.7676649
## 32: 0.004740574 -1.0188938 0.3891921 0.7676649
## 33: 0.004740574 -1.0188938 0.3891921 0.7676649
## 34: 0.004740574 -1.0188938 0.3891921 0.7676649
## 35: 0.004740574 -1.0188938 0.3891921 0.7676649
## 36: 0.004740574 -1.0188938 0.3891921 0.7676649
## 37: 0.004740574 -1.0188938 0.3891921 0.7676649
## 38: 0.005096736 -0.1004869 0.4195148 0.9429681
## 39: 0.005096736 -0.1004869 0.4195148 0.9429681
## 40: 0.005096736 -0.1004869 0.4195148 0.9429681
## 41: 0.005096736 -0.1004869 0.4195148 0.9429681
## 42: 0.005096736 -0.1004869 0.4195148 0.9429681
## 43: 0.005096736 -0.1004869 0.4195148 0.9429681
## 44: 0.004909730 -1.3643003 0.7964977 0.0290061
## 45: 0.004909730 -1.3643003 0.7964977 0.0290061
## 46: 0.004909730 -1.3643003 0.7964977 0.0290061
## 47: 0.004909730 -1.3643003 0.7964977 0.0290061
## 48: 0.004909730 -1.3643003 0.7964977 0.0290061
## 49: 0.004909730 -1.3643003 0.7964977 0.0290061
## 50: 0.004909730 -1.3643003 0.7964977 0.0290061
## 51: 0.004909730 -1.3643003 0.7964977 0.0290061
## 52: 0.004909730 -1.3643003 0.7964977 0.0290061
## 53: 0.004909730 -1.3643003 0.7964977 0.0290061
## 54: 0.004107492 -1.6060807 0.6281863 0.3548128
## 55: 0.004107492 -1.6060807 0.6281863 0.3548128
## 56: 0.004107492 -1.6060807 0.6281863 0.3548128
## 57: 0.004107492 -1.6060807 0.6281863 0.3548128
## 58: 0.004107492 -1.6060807 0.6281863 0.3548128
## 59: 0.004107492 -1.6060807 0.6281863 0.3548128
## 60: 0.004107492 -1.6060807 0.6281863 0.3548128
## 61: 0.004107492 -1.6060807 0.6281863 0.3548128
## 62: 0.004107492 -1.6060807 0.6281863 0.3548128
## 63: 0.004107492 -1.6060807 0.6281863 0.3548128
## 64: 0.004107492 -1.6060807 0.6281863 0.3548128
## 65: 0.004107492 -1.6060807 0.6281863 0.3548128
## 66: 0.004107492 -1.6060807 0.6281863 0.3548128
## 67: 0.004107492 -1.6060807 0.6281863 0.3548128
## 68: 0.004107492 -1.6060807 0.6281863 0.3548128
## 69: 0.004107492 -1.6060807 0.6281863 0.3548128
## 70: 0.004107492 -1.6060807 0.6281863 0.3548128
## 71: 0.004747012 -0.8916273 0.2737294 0.4292636
## 72: 0.004747012 -0.8916273 0.2737294 0.4292636
## 73: 0.004747012 -0.8916273 0.2737294 0.4292636
## 74: 0.004747012 -0.8916273 0.2737294 0.4292636
## 75: 0.004747012 -0.8916273 0.2737294 0.4292636
## 76: 0.004747012 -0.8916273 0.2737294 0.4292636
##           se.bp          v         c      pchi

##  [1] "ORF32" "ORF74" "ORF75" "ORF28" "ORF24" "ORF73" "ORF8"  "CTO"   "ORF76"
## [10] "ORF22" "ORF37" "ORF42" "ORF33" "ORF23" "ORF14"
## [1] 15
##  [1] "ORF1"    "ORF4"    "ORF7"    "ORF9"    "ORF17"   "ORF18"   "ORF20"  
##  [8] "ORF21"   "ORF24"   "ORF28"   "ORF31"   "ORF32"   "ORF34"   "ORF38"  
## [15] "ORF50"   "ORF61"   "ORF64_1" "ORF67_1" "ORF74"   "ORF75"   "NOIR_2" 
## [22] "ORF2"    "ORF3"    "ORF8"    "ORF11"   "ORF19"   "ORF22"   "ORF26"  
## [29] "ORF29"   "ORF36"   "ORF37"   "CTO"     "ORF40"   "ORF51"   "ORF66_1"
## [36] "ORF73"   "ORF76"   "ORF5"    "ORF30"   "ORF53"   "ORF63"   "ORF65_1"
## [43] "ORF69"   "ORF25"   "ORF35.5" "ORF43"   "ORF46"   "ORF58"   "ORF62"
## [1] 49

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  2:       1    ORF4 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  3:       1    ORF7 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  4:       1    ORF9 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  5:       1   ORF17 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  6:       1   ORF18 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  7:       1   ORF20 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  8:       1   ORF21 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  9:       1   ORF24 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 10:       1   ORF28 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 11:       1   ORF31 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 12:       1   ORF32 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 13:       1   ORF34 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 14:       1   ORF38 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 15:       1   ORF50 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 16:       1   ORF61 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 17:       1 ORF64_1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 18:       1 ORF67_1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 19:       1   ORF74 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 20:       1   ORF75 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 21:       1  NOIR_2 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 22:       2    ORF2 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 23:       2    ORF3 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 24:       2    ORF8 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 25:       2   ORF11 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 26:       2   ORF19 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 27:       2   ORF22 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 28:       2   ORF26 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 29:       2   ORF29 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 30:       2   ORF36 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 31:       2   ORF37 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 32:       2     CTO 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 33:       2   ORF40 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 34:       2   ORF51 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 35:       2 ORF66_1 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 36:       2   ORF73 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 37:       2   ORF76 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 38:       3    ORF5 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 39:       3 ORF65_1 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 40:       3   ORF69 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 41:       4    ORF6 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 42:       4   ORF13 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 43:       4   ORF15 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 44:       4   ORF16 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 45:       4   ORF33 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 46:       4   ORF42 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 47:       4   ORF52 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 48:       4   ORF54 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 49:       4   ORF60 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 50:       4   ORF72 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 51:       5   ORF10 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 52:       5   ORF12 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 53:       5   ORF14 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 54:       5   ORF23 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 55:       5   ORF27 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 56:       5   ORF35 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 57:       5   ORF39 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 58:       5   ORF41 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 59:       5   ORF44 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 60:       5   ORF48 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 61:       5   ORF49 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 62:       5   ORF57 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 63:       5   ORF59 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 64:       5  NOIR_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 65:       5   ORF68 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 66:       5   ORF70 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 67:       5   ORF71 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 68:       6   ORF25 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 69:       6 ORF35.5 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 70:       6   ORF43 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 71:       6   ORF46 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 72:       6   ORF58 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 73:       6   ORF62 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 74:       7   ORF30 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 75:       7   ORF53 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 76:       7   ORF63 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.005240502 -0.3857226 0.2263551 0.4554380
##  2: 0.005240502 -0.3857226 0.2263551 0.4554380
##  3: 0.005240502 -0.3857226 0.2263551 0.4554380
##  4: 0.005240502 -0.3857226 0.2263551 0.4554380
##  5: 0.005240502 -0.3857226 0.2263551 0.4554380
##  6: 0.005240502 -0.3857226 0.2263551 0.4554380
##  7: 0.005240502 -0.3857226 0.2263551 0.4554380
##  8: 0.005240502 -0.3857226 0.2263551 0.4554380
##  9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.005240502 -0.3857226 0.2263551 0.4554380
## 14: 0.005240502 -0.3857226 0.2263551 0.4554380
## 15: 0.005240502 -0.3857226 0.2263551 0.4554380
## 16: 0.005240502 -0.3857226 0.2263551 0.4554380
## 17: 0.005240502 -0.3857226 0.2263551 0.4554380
## 18: 0.005240502 -0.3857226 0.2263551 0.4554380
## 19: 0.005240502 -0.3857226 0.2263551 0.4554380
## 20: 0.005240502 -0.3857226 0.2263551 0.4554380
## 21: 0.005240502 -0.3857226 0.2263551 0.4554380
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.004740574 -1.0188938 0.3891921 0.7676649
## 25: 0.004740574 -1.0188938 0.3891921 0.7676649
## 26: 0.004740574 -1.0188938 0.3891921 0.7676649
## 27: 0.004740574 -1.0188938 0.3891921 0.7676649
## 28: 0.004740574 -1.0188938 0.3891921 0.7676649
## 29: 0.004740574 -1.0188938 0.3891921 0.7676649
## 30: 0.004740574 -1.0188938 0.3891921 0.7676649
## 31: 0.004740574 -1.0188938 0.3891921 0.7676649
## 32: 0.004740574 -1.0188938 0.3891921 0.7676649
## 33: 0.004740574 -1.0188938 0.3891921 0.7676649
## 34: 0.004740574 -1.0188938 0.3891921 0.7676649
## 35: 0.004740574 -1.0188938 0.3891921 0.7676649
## 36: 0.004740574 -1.0188938 0.3891921 0.7676649
## 37: 0.004740574 -1.0188938 0.3891921 0.7676649
## 38: 0.005096736 -0.1004869 0.4195148 0.9429681
## 39: 0.005096736 -0.1004869 0.4195148 0.9429681
## 40: 0.005096736 -0.1004869 0.4195148 0.9429681
## 41: 0.004909730 -1.3643003 0.7964977 0.0290061
## 42: 0.004909730 -1.3643003 0.7964977 0.0290061
## 43: 0.004909730 -1.3643003 0.7964977 0.0290061
## 44: 0.004909730 -1.3643003 0.7964977 0.0290061
## 45: 0.004909730 -1.3643003 0.7964977 0.0290061
## 46: 0.004909730 -1.3643003 0.7964977 0.0290061
## 47: 0.004909730 -1.3643003 0.7964977 0.0290061
## 48: 0.004909730 -1.3643003 0.7964977 0.0290061
## 49: 0.004909730 -1.3643003 0.7964977 0.0290061
## 50: 0.004909730 -1.3643003 0.7964977 0.0290061
## 51: 0.004107492 -1.6060807 0.6281863 0.3548128
## 52: 0.004107492 -1.6060807 0.6281863 0.3548128
## 53: 0.004107492 -1.6060807 0.6281863 0.3548128
## 54: 0.004107492 -1.6060807 0.6281863 0.3548128
## 55: 0.004107492 -1.6060807 0.6281863 0.3548128
## 56: 0.004107492 -1.6060807 0.6281863 0.3548128
## 57: 0.004107492 -1.6060807 0.6281863 0.3548128
## 58: 0.004107492 -1.6060807 0.6281863 0.3548128
## 59: 0.004107492 -1.6060807 0.6281863 0.3548128
## 60: 0.004107492 -1.6060807 0.6281863 0.3548128
## 61: 0.004107492 -1.6060807 0.6281863 0.3548128
## 62: 0.004107492 -1.6060807 0.6281863 0.3548128
## 63: 0.004107492 -1.6060807 0.6281863 0.3548128
## 64: 0.004107492 -1.6060807 0.6281863 0.3548128
## 65: 0.004107492 -1.6060807 0.6281863 0.3548128
## 66: 0.004107492 -1.6060807 0.6281863 0.3548128
## 67: 0.004107492 -1.6060807 0.6281863 0.3548128
## 68: 0.004747012 -0.8916273 0.2737294 0.4292636
## 69: 0.004747012 -0.8916273 0.2737294 0.4292636
## 70: 0.004747012 -0.8916273 0.2737294 0.4292636
## 71: 0.004747012 -0.8916273 0.2737294 0.4292636
## 72: 0.004747012 -0.8916273 0.2737294 0.4292636
## 73: 0.004747012 -0.8916273 0.2737294 0.4292636
## 74: 0.001974539 -2.6297796 0.6681400 0.6408455
## 75: 0.001974539 -2.6297796 0.6681400 0.6408455
## 76: 0.001974539 -2.6297796 0.6681400 0.6408455
##           se.bp          v         c      pchi

##  [1] "ORF32" "ORF74" "ORF75" "ORF28" "ORF24" "ORF73" "ORF8"  "CTO"   "ORF76"
## [10] "ORF22" "ORF37" "ORF42" "ORF33" "ORF23" "ORF14" "ORF63"
## [1] 16
##  [1] "ORF1"    "ORF4"    "ORF7"    "ORF9"    "ORF17"   "ORF18"   "ORF20"  
##  [8] "ORF21"   "ORF24"   "ORF28"   "ORF31"   "ORF32"   "ORF34"   "ORF38"  
## [15] "ORF50"   "ORF61"   "ORF64_1" "ORF67_1" "ORF74"   "ORF75"   "NOIR_2" 
## [22] "ORF2"    "ORF3"    "ORF8"    "ORF11"   "ORF19"   "ORF22"   "ORF26"  
## [29] "ORF29"   "ORF36"   "ORF37"   "CTO"     "ORF40"   "ORF51"   "ORF66_1"
## [36] "ORF73"   "ORF76"   "ORF5"    "ORF65_1" "ORF69"   "ORF25"   "ORF35.5"
## [43] "ORF43"   "ORF46"   "ORF58"   "ORF62"
## [1] 46

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  2:       1    ORF4 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  3:       1    ORF9 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  4:       1   ORF18 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  5:       1   ORF20 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  6:       1   ORF21 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  7:       1   ORF31 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  8:       1   ORF34 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  9:       1   ORF38 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 10:       1   ORF50 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 11:       1   ORF61 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 12:       1  NOIR_2 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 13:       2    ORF2 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 14:       2    ORF3 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 15:       2    ORF8 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 16:       2   ORF11 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 17:       2   ORF22 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 18:       2   ORF26 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 19:       2   ORF29 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 20:       2   ORF36 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 21:       2     CTO 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 22:       2   ORF40 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 23:       2   ORF73 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 24:       3    ORF5 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 25:       3 ORF65_1 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 26:       3   ORF69 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 27:       4    ORF6 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 28:       4   ORF13 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 29:       4   ORF15 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 30:       4   ORF16 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 31:       4   ORF33 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 32:       4   ORF42 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 33:       4   ORF52 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 34:       4   ORF54 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 35:       4   ORF60 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 36:       4   ORF72 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 37:       5    ORF7 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 38:       5   ORF17 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 39:       5   ORF24 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 40:       5   ORF28 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 41:       5   ORF32 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 42:       5 ORF64_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 43:       5 ORF67_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 44:       5   ORF74 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 45:       5   ORF75 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 46:       6   ORF10 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 47:       7   ORF12 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 48:       7   ORF14 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 49:       7   ORF23 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 50:       7   ORF27 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 51:       7   ORF35 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 52:       7   ORF39 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 53:       7   ORF41 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 54:       7   ORF44 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 55:       7   ORF48 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 56:       7   ORF49 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 57:       7   ORF57 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 58:       7   ORF59 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 59:       7  NOIR_1 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 60:       7   ORF68 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 61:       7   ORF70 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 62:       7   ORF71 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 63:       8   ORF19 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 64:       8   ORF37 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 65:       8   ORF51 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 66:       8 ORF66_1 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 67:       8   ORF76 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 68:       9   ORF25 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 69:       9 ORF35.5 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 70:       9   ORF43 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 71:       9   ORF46 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 72:       9   ORF58 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 73:       9   ORF62 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 74:      10   ORF30 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 75:      10   ORF53 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 76:      10   ORF63 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.005240502 -0.3857226 0.2263551 0.4554380
##  2: 0.005240502 -0.3857226 0.2263551 0.4554380
##  3: 0.005240502 -0.3857226 0.2263551 0.4554380
##  4: 0.005240502 -0.3857226 0.2263551 0.4554380
##  5: 0.005240502 -0.3857226 0.2263551 0.4554380
##  6: 0.005240502 -0.3857226 0.2263551 0.4554380
##  7: 0.005240502 -0.3857226 0.2263551 0.4554380
##  8: 0.005240502 -0.3857226 0.2263551 0.4554380
##  9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.004740574 -1.0188938 0.3891921 0.7676649
## 14: 0.004740574 -1.0188938 0.3891921 0.7676649
## 15: 0.004740574 -1.0188938 0.3891921 0.7676649
## 16: 0.004740574 -1.0188938 0.3891921 0.7676649
## 17: 0.004740574 -1.0188938 0.3891921 0.7676649
## 18: 0.004740574 -1.0188938 0.3891921 0.7676649
## 19: 0.004740574 -1.0188938 0.3891921 0.7676649
## 20: 0.004740574 -1.0188938 0.3891921 0.7676649
## 21: 0.004740574 -1.0188938 0.3891921 0.7676649
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.005096736 -0.1004869 0.4195148 0.9429681
## 25: 0.005096736 -0.1004869 0.4195148 0.9429681
## 26: 0.005096736 -0.1004869 0.4195148 0.9429681
## 27: 0.004909730 -1.3643003 0.7964977 0.0290061
## 28: 0.004909730 -1.3643003 0.7964977 0.0290061
## 29: 0.004909730 -1.3643003 0.7964977 0.0290061
## 30: 0.004909730 -1.3643003 0.7964977 0.0290061
## 31: 0.004909730 -1.3643003 0.7964977 0.0290061
## 32: 0.004909730 -1.3643003 0.7964977 0.0290061
## 33: 0.004909730 -1.3643003 0.7964977 0.0290061
## 34: 0.004909730 -1.3643003 0.7964977 0.0290061
## 35: 0.004909730 -1.3643003 0.7964977 0.0290061
## 36: 0.004909730 -1.3643003 0.7964977 0.0290061
## 37: 0.004107492 -1.6060807 0.6281863 0.3548128
## 38: 0.004107492 -1.6060807 0.6281863 0.3548128
## 39: 0.004107492 -1.6060807 0.6281863 0.3548128
## 40: 0.004107492 -1.6060807 0.6281863 0.3548128
## 41: 0.004107492 -1.6060807 0.6281863 0.3548128
## 42: 0.004107492 -1.6060807 0.6281863 0.3548128
## 43: 0.004107492 -1.6060807 0.6281863 0.3548128
## 44: 0.004107492 -1.6060807 0.6281863 0.3548128
## 45: 0.004107492 -1.6060807 0.6281863 0.3548128
## 46: 0.004747012 -0.8916273 0.2737294 0.4292636
## 47: 0.001974539 -2.6297796 0.6681400 0.6408455
## 48: 0.001974539 -2.6297796 0.6681400 0.6408455
## 49: 0.001974539 -2.6297796 0.6681400 0.6408455
## 50: 0.001974539 -2.6297796 0.6681400 0.6408455
## 51: 0.001974539 -2.6297796 0.6681400 0.6408455
## 52: 0.001974539 -2.6297796 0.6681400 0.6408455
## 53: 0.001974539 -2.6297796 0.6681400 0.6408455
## 54: 0.001974539 -2.6297796 0.6681400 0.6408455
## 55: 0.001974539 -2.6297796 0.6681400 0.6408455
## 56: 0.001974539 -2.6297796 0.6681400 0.6408455
## 57: 0.001974539 -2.6297796 0.6681400 0.6408455
## 58: 0.001974539 -2.6297796 0.6681400 0.6408455
## 59: 0.001974539 -2.6297796 0.6681400 0.6408455
## 60: 0.001974539 -2.6297796 0.6681400 0.6408455
## 61: 0.001974539 -2.6297796 0.6681400 0.6408455
## 62: 0.001974539 -2.6297796 0.6681400 0.6408455
## 63: 0.003927220 -1.7307215 0.6541499 0.4863678
## 64: 0.003927220 -1.7307215 0.6541499 0.4863678
## 65: 0.003927220 -1.7307215 0.6541499 0.4863678
## 66: 0.003927220 -1.7307215 0.6541499 0.4863678
## 67: 0.003927220 -1.7307215 0.6541499 0.4863678
## 68: 0.004045947 -1.1019554 0.1437770 0.6282165
## 69: 0.004045947 -1.1019554 0.1437770 0.6282165
## 70: 0.004045947 -1.1019554 0.1437770 0.6282165
## 71: 0.004045947 -1.1019554 0.1437770 0.6282165
## 72: 0.004045947 -1.1019554 0.1437770 0.6282165
## 73: 0.004045947 -1.1019554 0.1437770 0.6282165
## 74: 0.005256888 -0.8090952 0.6096982 0.4091181
## 75: 0.005256888 -0.8090952 0.6096982 0.4091181
## 76: 0.005256888 -0.8090952 0.6096982 0.4091181
##           se.bp          v         c      pchi

##  [1] "ORF42"   "ORF33"   "ORF67_1" "ORF39"   "ORF23"   "ORF35"   "NOIR_1" 
##  [8] "ORF14"   "ORF76"   "ORF63"
## [1] 10
##  [1] "ORF1"    "ORF4"    "ORF9"    "ORF18"   "ORF20"   "ORF21"   "ORF31"  
##  [8] "ORF34"   "ORF38"   "ORF50"   "ORF61"   "NOIR_2"  "ORF2"    "ORF3"   
## [15] "ORF8"    "ORF11"   "ORF22"   "ORF26"   "ORF29"   "ORF36"   "CTO"    
## [22] "ORF40"   "ORF73"   "ORF5"    "ORF65_1" "ORF69"   "ORF10"   "ORF25"  
## [29] "ORF35.5" "ORF43"   "ORF46"   "ORF58"   "ORF62"   "ORF30"   "ORF53"  
## [36] "ORF63"
## [1] 36

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  2:       1    ORF4 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  3:       1    ORF9 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  4:       1   ORF18 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  5:       1   ORF20 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  6:       1   ORF21 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  7:       1   ORF31 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  8:       1   ORF34 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  9:       1   ORF38 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 10:       1   ORF50 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 11:       1   ORF61 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 12:       1  NOIR_2 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 13:       2    ORF2 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 14:       2    ORF3 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 15:       2    ORF8 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 16:       2   ORF11 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 17:       2   ORF22 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 18:       2   ORF26 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 19:       2   ORF29 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 20:       2   ORF36 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 21:       2     CTO 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 22:       2   ORF40 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 23:       2   ORF73 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 24:       3    ORF5 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 25:       3 ORF65_1 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 26:       3   ORF69 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 27:       4    ORF6 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 28:       4   ORF13 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 29:       4   ORF33 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 30:       4   ORF42 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 31:       5    ORF7 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 32:       5   ORF17 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 33:       5   ORF24 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 34:       5   ORF28 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 35:       5   ORF32 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 36:       5 ORF64_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 37:       5 ORF67_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 38:       5   ORF74 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 39:       5   ORF75 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 40:       6   ORF10 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 41:       7   ORF12 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 42:       7   ORF27 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 43:       7   ORF35 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 44:       7   ORF41 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 45:       7   ORF44 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 46:       7   ORF49 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 47:       7   ORF59 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 48:       7  NOIR_1 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 49:       7   ORF70 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 50:       8   ORF14 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 51:       8   ORF23 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 52:       8   ORF39 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 53:       8   ORF48 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 54:       8   ORF57 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 55:       8   ORF68 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 56:       8   ORF71 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 57:       9   ORF15 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 58:       9   ORF16 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 59:       9   ORF52 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 60:       9   ORF54 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 61:       9   ORF60 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 62:       9   ORF72 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 63:      10   ORF19 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 64:      10   ORF37 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 65:      10   ORF51 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 66:      10 ORF66_1 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 67:      10   ORF76 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 68:      11   ORF25 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 69:      11 ORF35.5 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 70:      11   ORF43 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 71:      11   ORF46 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 72:      11   ORF58 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 73:      11   ORF62 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 74:      12   ORF30 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
## 75:      12   ORF53 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
## 76:      12   ORF63 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.005240502 -0.3857226 0.2263551 0.4554380
##  2: 0.005240502 -0.3857226 0.2263551 0.4554380
##  3: 0.005240502 -0.3857226 0.2263551 0.4554380
##  4: 0.005240502 -0.3857226 0.2263551 0.4554380
##  5: 0.005240502 -0.3857226 0.2263551 0.4554380
##  6: 0.005240502 -0.3857226 0.2263551 0.4554380
##  7: 0.005240502 -0.3857226 0.2263551 0.4554380
##  8: 0.005240502 -0.3857226 0.2263551 0.4554380
##  9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.004740574 -1.0188938 0.3891921 0.7676649
## 14: 0.004740574 -1.0188938 0.3891921 0.7676649
## 15: 0.004740574 -1.0188938 0.3891921 0.7676649
## 16: 0.004740574 -1.0188938 0.3891921 0.7676649
## 17: 0.004740574 -1.0188938 0.3891921 0.7676649
## 18: 0.004740574 -1.0188938 0.3891921 0.7676649
## 19: 0.004740574 -1.0188938 0.3891921 0.7676649
## 20: 0.004740574 -1.0188938 0.3891921 0.7676649
## 21: 0.004740574 -1.0188938 0.3891921 0.7676649
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.005096736 -0.1004869 0.4195148 0.9429681
## 25: 0.005096736 -0.1004869 0.4195148 0.9429681
## 26: 0.005096736 -0.1004869 0.4195148 0.9429681
## 27: 0.004909730 -1.3643003 0.7964977 0.0290061
## 28: 0.004909730 -1.3643003 0.7964977 0.0290061
## 29: 0.004909730 -1.3643003 0.7964977 0.0290061
## 30: 0.004909730 -1.3643003 0.7964977 0.0290061
## 31: 0.004107492 -1.6060807 0.6281863 0.3548128
## 32: 0.004107492 -1.6060807 0.6281863 0.3548128
## 33: 0.004107492 -1.6060807 0.6281863 0.3548128
## 34: 0.004107492 -1.6060807 0.6281863 0.3548128
## 35: 0.004107492 -1.6060807 0.6281863 0.3548128
## 36: 0.004107492 -1.6060807 0.6281863 0.3548128
## 37: 0.004107492 -1.6060807 0.6281863 0.3548128
## 38: 0.004107492 -1.6060807 0.6281863 0.3548128
## 39: 0.004107492 -1.6060807 0.6281863 0.3548128
## 40: 0.004747012 -0.8916273 0.2737294 0.4292636
## 41: 0.001974539 -2.6297796 0.6681400 0.6408455
## 42: 0.001974539 -2.6297796 0.6681400 0.6408455
## 43: 0.001974539 -2.6297796 0.6681400 0.6408455
## 44: 0.001974539 -2.6297796 0.6681400 0.6408455
## 45: 0.001974539 -2.6297796 0.6681400 0.6408455
## 46: 0.001974539 -2.6297796 0.6681400 0.6408455
## 47: 0.001974539 -2.6297796 0.6681400 0.6408455
## 48: 0.001974539 -2.6297796 0.6681400 0.6408455
## 49: 0.001974539 -2.6297796 0.6681400 0.6408455
## 50: 0.003927220 -1.7307215 0.6541499 0.4863678
## 51: 0.003927220 -1.7307215 0.6541499 0.4863678
## 52: 0.003927220 -1.7307215 0.6541499 0.4863678
## 53: 0.003927220 -1.7307215 0.6541499 0.4863678
## 54: 0.003927220 -1.7307215 0.6541499 0.4863678
## 55: 0.003927220 -1.7307215 0.6541499 0.4863678
## 56: 0.003927220 -1.7307215 0.6541499 0.4863678
## 57: 0.004045947 -1.1019554 0.1437770 0.6282165
## 58: 0.004045947 -1.1019554 0.1437770 0.6282165
## 59: 0.004045947 -1.1019554 0.1437770 0.6282165
## 60: 0.004045947 -1.1019554 0.1437770 0.6282165
## 61: 0.004045947 -1.1019554 0.1437770 0.6282165
## 62: 0.004045947 -1.1019554 0.1437770 0.6282165
## 63: 0.005256888 -0.8090952 0.6096982 0.4091181
## 64: 0.005256888 -0.8090952 0.6096982 0.4091181
## 65: 0.005256888 -0.8090952 0.6096982 0.4091181
## 66: 0.005256888 -0.8090952 0.6096982 0.4091181
## 67: 0.005256888 -0.8090952 0.6096982 0.4091181
## 68: 0.003699662 -1.7457057 0.5965758 0.2636889
## 69: 0.003699662 -1.7457057 0.5965758 0.2636889
## 70: 0.003699662 -1.7457057 0.5965758 0.2636889
## 71: 0.003699662 -1.7457057 0.5965758 0.2636889
## 72: 0.003699662 -1.7457057 0.5965758 0.2636889
## 73: 0.003699662 -1.7457057 0.5965758 0.2636889
## 74: 0.003612836 -1.5562853 0.3815687 0.4734673
## 75: 0.003612836 -1.5562853 0.3815687 0.4734673
## 76: 0.003612836 -1.5562853 0.3815687 0.4734673
##           se.bp          v         c      pchi

##  [1] "ORF75"   "ORF32"   "ORF67_1" "ORF28"   "ORF24"   "ORF14"   "ORF57"  
##  [8] "ORF76"   "ORF62"   "ORF63"
## [1] 10
##  [1] "ORF1"    "ORF4"    "ORF9"    "ORF18"   "ORF20"   "ORF21"   "ORF31"  
##  [8] "ORF34"   "ORF38"   "ORF50"   "ORF61"   "NOIR_2"  "ORF2"    "ORF3"   
## [15] "ORF8"    "ORF11"   "ORF22"   "ORF26"   "ORF29"   "ORF36"   "CTO"    
## [22] "ORF40"   "ORF73"   "ORF5"    "ORF65_1" "ORF69"   "ORF10"   "ORF15"  
## [29] "ORF16"   "ORF52"   "ORF54"   "ORF60"   "ORF72"   "ORF19"   "ORF37"  
## [36] "ORF51"   "ORF66_1" "ORF76"
## [1] 38

Selected number of clusters: 12

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  2:       1    ORF4 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  3:       1    ORF9 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  4:       1   ORF18 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  5:       1   ORF20 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  6:       1   ORF21 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  7:       1   ORF31 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  8:       1   ORF34 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
##  9:       1   ORF38 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 10:       1   ORF50 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 11:       1   ORF61 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 12:       1  NOIR_2 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 13:       2    ORF2 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 14:       2    ORF3 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 15:       2    ORF8 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 16:       2   ORF11 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 17:       2   ORF22 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 18:       2   ORF26 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 19:       2   ORF29 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 20:       2   ORF36 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 21:       2     CTO 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 22:       2   ORF40 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 23:       2   ORF73 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 24:       3    ORF5 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 25:       3 ORF65_1 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 26:       3   ORF69 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 27:       4    ORF6 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 28:       4   ORF13 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 29:       4   ORF33 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 30:       4   ORF42 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 31:       5    ORF7 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 32:       5   ORF17 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 33:       5   ORF24 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 34:       5   ORF28 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 35:       5   ORF32 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 36:       5 ORF64_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 37:       5 ORF67_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 38:       5   ORF74 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 39:       5   ORF75 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 40:       6   ORF10 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 41:       7   ORF12 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 42:       7   ORF27 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 43:       7   ORF35 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 44:       7   ORF41 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 45:       7   ORF44 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 46:       7   ORF49 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 47:       7   ORF59 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 48:       7  NOIR_1 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 49:       7   ORF70 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 50:       8   ORF14 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 51:       8   ORF23 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 52:       8   ORF39 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 53:       8   ORF48 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 54:       8   ORF57 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 55:       8   ORF68 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 56:       8   ORF71 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 57:       9   ORF15 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 58:       9   ORF16 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 59:       9   ORF52 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 60:       9   ORF54 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 61:       9   ORF60 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 62:       9   ORF72 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 63:      10   ORF19 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 64:      10   ORF37 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 65:      10   ORF51 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 66:      10 ORF66_1 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 67:      10   ORF76 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 68:      11   ORF25 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 69:      11 ORF35.5 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 70:      11   ORF43 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 71:      11   ORF46 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 72:      11   ORF58 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 73:      11   ORF62 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 74:      12   ORF30 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
## 75:      12   ORF53 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
## 76:      12   ORF63 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.005240502 -0.3857226 0.2263551 0.4554380
##  2: 0.005240502 -0.3857226 0.2263551 0.4554380
##  3: 0.005240502 -0.3857226 0.2263551 0.4554380
##  4: 0.005240502 -0.3857226 0.2263551 0.4554380
##  5: 0.005240502 -0.3857226 0.2263551 0.4554380
##  6: 0.005240502 -0.3857226 0.2263551 0.4554380
##  7: 0.005240502 -0.3857226 0.2263551 0.4554380
##  8: 0.005240502 -0.3857226 0.2263551 0.4554380
##  9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.004740574 -1.0188938 0.3891921 0.7676649
## 14: 0.004740574 -1.0188938 0.3891921 0.7676649
## 15: 0.004740574 -1.0188938 0.3891921 0.7676649
## 16: 0.004740574 -1.0188938 0.3891921 0.7676649
## 17: 0.004740574 -1.0188938 0.3891921 0.7676649
## 18: 0.004740574 -1.0188938 0.3891921 0.7676649
## 19: 0.004740574 -1.0188938 0.3891921 0.7676649
## 20: 0.004740574 -1.0188938 0.3891921 0.7676649
## 21: 0.004740574 -1.0188938 0.3891921 0.7676649
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.005096736 -0.1004869 0.4195148 0.9429681
## 25: 0.005096736 -0.1004869 0.4195148 0.9429681
## 26: 0.005096736 -0.1004869 0.4195148 0.9429681
## 27: 0.004909730 -1.3643003 0.7964977 0.0290061
## 28: 0.004909730 -1.3643003 0.7964977 0.0290061
## 29: 0.004909730 -1.3643003 0.7964977 0.0290061
## 30: 0.004909730 -1.3643003 0.7964977 0.0290061
## 31: 0.004107492 -1.6060807 0.6281863 0.3548128
## 32: 0.004107492 -1.6060807 0.6281863 0.3548128
## 33: 0.004107492 -1.6060807 0.6281863 0.3548128
## 34: 0.004107492 -1.6060807 0.6281863 0.3548128
## 35: 0.004107492 -1.6060807 0.6281863 0.3548128
## 36: 0.004107492 -1.6060807 0.6281863 0.3548128
## 37: 0.004107492 -1.6060807 0.6281863 0.3548128
## 38: 0.004107492 -1.6060807 0.6281863 0.3548128
## 39: 0.004107492 -1.6060807 0.6281863 0.3548128
## 40: 0.004747012 -0.8916273 0.2737294 0.4292636
## 41: 0.001974539 -2.6297796 0.6681400 0.6408455
## 42: 0.001974539 -2.6297796 0.6681400 0.6408455
## 43: 0.001974539 -2.6297796 0.6681400 0.6408455
## 44: 0.001974539 -2.6297796 0.6681400 0.6408455
## 45: 0.001974539 -2.6297796 0.6681400 0.6408455
## 46: 0.001974539 -2.6297796 0.6681400 0.6408455
## 47: 0.001974539 -2.6297796 0.6681400 0.6408455
## 48: 0.001974539 -2.6297796 0.6681400 0.6408455
## 49: 0.001974539 -2.6297796 0.6681400 0.6408455
## 50: 0.003927220 -1.7307215 0.6541499 0.4863678
## 51: 0.003927220 -1.7307215 0.6541499 0.4863678
## 52: 0.003927220 -1.7307215 0.6541499 0.4863678
## 53: 0.003927220 -1.7307215 0.6541499 0.4863678
## 54: 0.003927220 -1.7307215 0.6541499 0.4863678
## 55: 0.003927220 -1.7307215 0.6541499 0.4863678
## 56: 0.003927220 -1.7307215 0.6541499 0.4863678
## 57: 0.004045947 -1.1019554 0.1437770 0.6282165
## 58: 0.004045947 -1.1019554 0.1437770 0.6282165
## 59: 0.004045947 -1.1019554 0.1437770 0.6282165
## 60: 0.004045947 -1.1019554 0.1437770 0.6282165
## 61: 0.004045947 -1.1019554 0.1437770 0.6282165
## 62: 0.004045947 -1.1019554 0.1437770 0.6282165
## 63: 0.005256888 -0.8090952 0.6096982 0.4091181
## 64: 0.005256888 -0.8090952 0.6096982 0.4091181
## 65: 0.005256888 -0.8090952 0.6096982 0.4091181
## 66: 0.005256888 -0.8090952 0.6096982 0.4091181
## 67: 0.005256888 -0.8090952 0.6096982 0.4091181
## 68: 0.003699662 -1.7457057 0.5965758 0.2636889
## 69: 0.003699662 -1.7457057 0.5965758 0.2636889
## 70: 0.003699662 -1.7457057 0.5965758 0.2636889
## 71: 0.003699662 -1.7457057 0.5965758 0.2636889
## 72: 0.003699662 -1.7457057 0.5965758 0.2636889
## 73: 0.003699662 -1.7457057 0.5965758 0.2636889
## 74: 0.003612836 -1.5562853 0.3815687 0.4734673
## 75: 0.003612836 -1.5562853 0.3815687 0.4734673
## 76: 0.003612836 -1.5562853 0.3815687 0.4734673
##           se.bp          v         c      pchi

##  [1] "ORF75"   "ORF32"   "ORF67_1" "ORF28"   "ORF24"   "ORF14"   "ORF57"  
##  [8] "ORF76"   "ORF62"   "ORF63"
## [1] 10
##  [1] "ORF1"    "ORF4"    "ORF9"    "ORF18"   "ORF20"   "ORF21"   "ORF31"  
##  [8] "ORF34"   "ORF38"   "ORF50"   "ORF61"   "NOIR_2"  "ORF2"    "ORF3"   
## [15] "ORF8"    "ORF11"   "ORF22"   "ORF26"   "ORF29"   "ORF36"   "CTO"    
## [22] "ORF40"   "ORF73"   "ORF5"    "ORF65_1" "ORF69"   "ORF10"   "ORF15"  
## [29] "ORF16"   "ORF52"   "ORF54"   "ORF60"   "ORF72"   "ORF19"   "ORF37"  
## [36] "ORF51"   "ORF66_1" "ORF76"
## [1] 38

Remove genes from clusters ?

##  [1] "ORF1"    "ORF4"    "ORF9"    "ORF18"   "ORF20"   "ORF21"   "ORF31"  
##  [8] "ORF34"   "ORF38"   "ORF50"   "ORF61"   "NOIR_2"  "ORF2"    "ORF3"   
## [15] "ORF8"    "ORF11"   "ORF22"   "ORF26"   "ORF29"   "ORF36"   "CTO"    
## [22] "ORF40"   "ORF73"   "ORF5"    "ORF65_1" "ORF69"   "ORF10"   "ORF15"  
## [29] "ORF16"   "ORF52"   "ORF54"   "ORF60"   "ORF72"   "ORF19"   "ORF37"  
## [36] "ORF51"   "ORF66_1" "ORF76"
## [1] 38
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       1    12
##  2:       2    11
##  3:       5     9
##  4:       7     9
##  5:       8     7
##  6:       9     6
##  7:      11     6
##  8:      10     5
##  9:       4     4
## 10:       3     3
## 11:      12     3
## 12:       6     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters